Food and beer and sunshine.....sounds bloody good to me!
Don't waste your time on Alcatraz. It's a total dump. Very depressing. I dunno why I went. I suppose it's because I watched them silly Clint Eastwood films like everybody else and there's hype around the place because of that, but history of the place is sad and the whole place exudes stupidity. But it's a former jail site, what do you expect, nothing really interesting at all, looking at all them empty cells.
If you want to take a boat ride, there are other ones that cruise around the Bay that are much more interesting and pretty than going over to an old dirty prison site.
Getting a car is a nice way to see the town. Going up to Twin Peaks you can see the whole city from the geometric centre overlooking the entire area.
You can also do a massive circular drive around the entire Bay Area on the freeways and hit all the bridges that crisscross, I even went and did it both directions because at the time the Bay bridge was double deck and one way you drive up on top and the other way you drive on the bottom. Of course you have to do the same with the Golden Gate Bridge going both directions.
Of course you must drive down Lombard Street from the top down (one way street) and do the famous snaky drive down the hill.
If your focus is on the City and like art and exhibits, the new museums are very nice. The Science one is excellent.
If you have time to get out of the City and drive to other smaller ones of course you must try to get up to Marin country,
If you are a fan of Star Wars go to the Presidio
http://sftodo.com/blog/2012/01/24/star-wars-lucasfilm-san-francisco.html
This covers the rest of California as well but if you can get up to the Redwoods it is amazing
http://www.visitcalifornia.com/feature/diy-star-wars-experiences-california